title: Leukopak_Control_B044-P2_IMM19_416

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Genome_build: Ensembl GRCh38-3.0.0
Supplementary_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

value: Healthy

tag: Sex

tag: visit


title: Leukopak_Control_B044-P1_IMM19_416

status: Public on May 30 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: male


title: Hematopoetic_CD8T_37

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

data_processing:
The resulting read count matrix was passed through robust QC procedure to remove ROIs of low surface area (<5000 µm2) or low perfect aligned reads (< 80%), and probes of low quality or identified as global or local outliers (fails Grubbs outlier test in ≥ 20% segments). Genes differentially expressed between groups of interest were detected using gene-wise linear modeling in R (limma, v3.50.3), with p-value adjusted for false discovery rate.
FASTQ files were decoded using a Nanostring  GeoMx NGS pipeline app version 2.0.21
Assembly: HGR38
Supplementary files format and content: normalized matrix count
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: synovium

growth_protocol: Back paws were decalcified in 14% of EDTA for two weeks before being embedded in paraffin. Then,  4 um-thick  parafin sections were stained with human anti CD45 and Human anti CD8 T cells. Stained slides were loaded and scanned onto a GeoMx instrument.

extract_protocol:
Stained slides were loaded and scanned onto a GeoMx instrument.Seven Regions of interest (ROI) were selected based on the CD45 and CD8 fluorescent staining and auto-segmentation algorithm. RNA was isolated using Agilent RNA isolation kit with manufactured recommended protocol.
Photocleaved oligonucleotides from the ROI were collected and products were processed and sequenced on an Illumina NextSeq 2000. The ROI were selected based on the positive staining of CD8 and CD45

treatment_protocol: The slides were processedfollowing the NanoString protocols as documented in Manual Slide Preparation MAN-10150-01.The slides were stained with antibodies specific for human anti-CD8 (EPR21769, AbCam) and anti-CD45 (EM-05, Novus).

tag: tissue

value: synovium

tag: cell type

value: Hematopoietic cells (CD45+/CD8+/CD8-)

tag: roi lot

value: collect slide 3

tag: condition

value: PsA


title: Leukopak_Control_B038-P2_IMM19_411


title: Hematopoetic_CD8T_36


title: Leukopak_Control_B038-P1_IMM19_411


title: Hematopoetic_CD8T_33

value: collect slide 2

value: Control


title: Hematopoetic_CD8T_35


title: Hematopoetic_CD8T_34


title: Leukopak_Control_B037-P2_IMM19_410


title: Leukopak_Control_B037-P1_IMM19_410


title: Hematopoetic_CD8T_32


title: Leukopak_Control_B033-P1_IMM19_408


title: Leukopak_Control_B027-P2_IMM19_406


title: Leukopak_Control_B033-P2_IMM19_408


title: Hematopoetic_CD8T_30


title: Hematopoetic_CD8T_31


title: Hematopoetic_CD8T_29


title: Hematopoetic_CD8T_28


title: Leukopak_Control_B027-P1_IMM19_406


title: Leukopak_Control_B025-P2_IMM19_404


title: Leukopak_Control_B025-P1_IMM19_404


title: Hematopoetic_CD8T_26


title: Hematopoetic_CD8T_25


title: Leukopak_Control_B024-P1_IMM19_403


title: Leukopak_Control_B011-P1_IMM19_395


title: Leukopak_Control_B021-P1_IMM19_401


title: Hematopoetic_CD8T_22


title: Hematopoetic_CD8T_23


title: Hematopoetic_CD8T_21


title: Covid_male_42409_4_B044_ATAC

library_source: genomic

molecule: genomic DNA

tag: disease

value: Visit 4


title: Hematopoetic_CD8T_20


title: Hematopoetic_CD8T_19


title: Covid_female_32054_4_B044_ATAC

value: female


title: Covid_male_32416_4_B044_ATAC


title: Hematopoetic_CD8T_27


title: Hematopoetic_CD8T_81

value: collect slide 4


title: Covid_female_32245_4_B044_ATAC


title: Hematopoetic_CD8T_80

value: collect slide 1


title: Hematopoetic_CD8T_79


title: Covid_male_32131_4_B044_ATAC


title: Hematopoetic_CD8T_77


title: Hematopoetic_CD8T_78


title: Leukopak_Control_B024-P2_IMM19_403


title: Covid_female_31945_4_B044_ATAC


title: Covid_male_32415_3_B044_ATAC

value: Visit 3


title: Hematopoetic_CD8T_24


title: Hematopoetic_CD8T_13

value: collect slide 6

value: Ps


title: Healthy_female_11096_1_B044_ATAC

value: Visit 1


title: Hematopoetic_CD8T_76


title: Covid_male_32209_4_B044_ATAC


title: Covid_female_32140_4_B044_ATAC


title: Hematopoetic_CD8T_74


title: Healthy_male_11872_1_B044_ATAC


title: Hematopoetic_CD8T_73


title: Hematopoetic_CD8T_75


title: Covid_male_42409_3_B044_ATAC


title: Covid_male_32415_4_B044_ATAC


title: Hematopoetic_CD8T_71


title: Covid_female_32255_4_B044_ATAC


title: Hematopoetic_CD8T_72


title: Covid_male_32251_4_B038_ATAC


title: Covid_male_32416_3_B044_ATAC


title: Covid_female_32196_1_B038_ATAC


title: Healthy_male_11160_1_B038_ATAC


title: Hematopoetic_CD8T_68


title: Hematopoetic_CD8T_69


title: Covid_male_32415_2_B038_ATAC

value: Visit 2


title: Hematopoetic_CD8T_67


title: Covid_male_42409_2_B038_ATAC


title: Prol_SCR_rep3

city: Pittsburgh

first: David

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using STAR, with options --outFilterMismatchNoverReadLmax 0.02 and --outFilterMultimapNmax 1
Aligned reads were processed in deepTools by using the bamCoverage command to generate stranded bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Assembly: mm10
Supplementary files format and content: bigwig

source_name: cell line

growth_protocol: Myoblasts were grown and differentiated on plates coated with 0.02% collagen (Advanced BioMatrix, Carlsbad, CA, USA). For the proliferation condition, the myoblasts were cultured in growth medium [1:1 v/v DMEM:F-12, 20% fetal bovine serum(FBS), and 25 ng/ml of basic fibroblast growth factor (FGF) for 48 h. To induce differentiation, the cells were allowed to reach 90% confluency and changed into differentiation medium (DMEM) containing 2% horse serum supplemented with insulin.

extract_protocol:
RNA was extracted from flash-frozen cell pellets with TRIzol per manufacturer's instructions.
RNA-seq; built with NEBNext Directional kit

treatment_protocol: To infect primary myoblasts, 5 ml of filtered lentiviral supernatant was supplemented with 8 μg/ml polybrene (Sigma) were used to transduce 2 × 10^6 cells. After overnight incubation, infected cells were then selected in growth media containing 2 μg/ml puromycin (Invitrogen). Stable myoblasts were maintained in growth media containing 1 μg/ml puromycin.

value: cell line

value: Proliferating myoblast

tag: genotype

value: SCR KO


title: Covid_male_32416_2_B038_ATAC

value: male


title: Prol_SCR_rep1


title: Diff_SCR_rep2

value: Differentiating myoblast


title: Prol_SCR_rep2


title: Diff_SCR_rep1


title: Prol_CRIP2_rep2

value: CRIP2 KO


title: Covid_female_32196_2_B038_ATAC


title: Diff_CRIP2_rep2


title: Prol_CRIP2_rep1


title: Healthy_female_11085_1_B038_ATAC

value: Healthy


title: Covid_female_32220_4_B038_ATAC


title: Hematopoetic_CD8T_70

value: synovium

value: Hematopoietic cells (CD45+/CD8+/CD8-)

value: Control


title: Diff_CRIP2_rep1


title: Covid_male_42409_1_B038_ATAC


title: Prol_rep3_NT_IgG

data_processing:
Reads trimmed to 25 bp
Reads aligned to hg38 using bowtie2 (options -q -N -X 1000 -I 50 --no-unal)
Aligned reads were deduplicated using Picard and quality-filtered using SAMtools (MAPQ ≥ 10)
Filtered reads were size-selected to separate factor-sized footprints (1-120 bp) using awk.
Size-selected reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 5 bp bins with normalization to 1X coverage and 20-bp smoothing.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Primary myoblast cells

extract_protocol: Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodies followed by proteinA/proteinG-MNase. Cleavage of Mnase was initiated by Ca2+ addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

treatment_protocol: Differentiating myoblasts were treated with Cu, Insulin, or no treatment, while proliferating myoblasts were treated with either Cu or no treatment.

value: Primary myoblast cells

tag: treatment

value: No treatment


title: Covid_female_32124_3_B038_ATAC

value: female

value: Visit 3


title: Covid_female_32140_3_B038_ATAC


title: Covid_male_32416_1_B038_ATAC


title: Covid_male_32209_3_B037_ATAC


title: Covid_female_32196_3_B038_ATAC


title: Covid_female_32255_2_B037_ATAC


title: Covid_female_32245_2_B037_ATAC


title: Prol_rep3_Cu_CRIP2

value: Cu-treated


title: Prol_rep2_NT_CRIP2


title: Covid_male_32209_1_B037_ATAC

value: Visit 1


title: Covid_female_32245_3_B037_ATAC


title: Covid_male_32415_1_B038_ATAC


title: Prol_rep2_NT_IgG


title: Prol_rep2_Cu_IgG


title: Prol_rep2_Cu_CRIP2


title: Prol_rep1_NT_CRIP2


title: Healthy_female_11534_1_B037_ATAC


title: Covid_male_32209_2_B037_ATAC

value: Visit 2


title: Prol_rep1_Cu_IgG


title: Prol_rep1_Cu_CRIP2


title: Prol_rep3_NT_CRIP2


title: Diff_rep3_NT_IgG


title: Covid_female_32255_1_B037_ATAC


title: Covid_male_32131_2_B037_ATAC


title: Covid_female_32255_3_B037_ATAC


title: Prol_rep3_Cu_IgG


title: Covid_female_32038_5_B037_ATAC

value: Visit 5


title: Diff_rep3_Cu_CRIP2


title: Covid_male_32131_1_B037_ATAC


title: Covid_male_32131_3_B037_ATAC


title: Diff_rep3_Ins_CRIP2

value: Insulin-treated


title: Diff_rep2_Ins_IgG


title: Covid_female_32220_3_B033_ATAC


title: Diff_rep3_Cu_IgG


title: Diff_rep2_Ins_CRIP2


title: Diff_rep2_Cu_IgG


title: Healthy_male_11090_1_B037_ATAC


title: Prol_rep1_NT_IgG

value: Proliferating myoblast


title: Covid_male_31874_4_B037_ATAC

value: male

value: Visit 4


title: Covid_female_31945_1_B033_ATAC


title: Diff_rep2_Cu_CRIP2

value: Differentiating myoblast


title: Healthy_female_11776_1_B033_ATAC

value: Healthy


title: Covid_female_31945_2_B033_ATAC


title: Healthy_female_11224_1_B033_ATAC


title: Diff_rep1_NT_CRIP2


title: Diff_rep1_NT_IgG


title: Diff_rep1_Ins_IgG


title: Covid_male_32251_3_B033_ATAC


title: Diff_rep2_NT_CRIP2


title: Covid_female_31945_3_B033_ATAC


title: Covid_female_32038_4_B033_ATAC


title: Covid_female_32140_2_B027_ATAC


title: Diff_rep1_Ins_CRIP2


title: Diff_rep1_Cu_CRIP2


title: CON2lane2

city: Leuven

first: Tine

last: Wils

state: Vlaams-Brabant

address: Herestraat 49 - box 811

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

description:
GC111380
10X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger Software 5.0.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab seperated files and matrix files

molecule: polyA RNA

source_name: Nasal Inferior Turbinate

extract_protocol:
Single cell suspension of surgically collected inferior turbinates were obtained by enzymatic digestion using liberase (87.5 µg/ml, 5401127001, Roche) and DNase I (300 µg/ml, 10104159001, Roche) in RPMI with 10% FBS for 30’ with additional mechanical disruption using a 16G needle after both 15’ and 30’ of enzymatic digestion. Digestion was stopped by adding EDTA (20 mM, 15575020, Invitrogen), whereafter red blood cells were lysed using 9.9% NaCl solution. Negative selection for immune, myeloid and fibroblast was performed using anti-CD45 (11153D, Invitrogen), anti-CD15 (11137D, Invitrogen) and anti-CD31 (11155D, Invitrogen) dynabeads, respectively. Cells were resuspended in PBS and filtered through a 70 μm cell strainer (542070, Greiner).
Library construction was performed according to manufacture's guidelines (singe cell 3' v2 protocol, 10X genomics)

value: Nasal Inferior Turbinate

tag: subject status

value: control


title: Covid_female_32054_3_B027_ATAC


title: CON2lane1

description:
GC111379
10X genomics


title: Covid_female_32054_2_B027_ATAC


title: Covid_female_32140_1_B027_ATAC


title: CON1lane2

description:
GC111378
10X genomics


title: CON1lane1

description:
GC111377
10X genomics


title: Diff_rep2_NT_IgG


title: AR2lane2

description:
GC111202
10X genomics

value: individual with house dust mite-induced allergic rhinitis


title: Covid_male_32251_1_B027_ATAC


title: Covid_female_32124_2_B027_ATAC


title: Covid_male_32251_2_B027_ATAC


title: Covid_female_32054_1_B027_ATAC


title: AR1lane2

description:
GC111200
10X genomics


title: Covid_female_32124_1_B027_ATAC


title: AR1lane1

description:
GC111199
10X genomics


title: CAF47

city: Suwon-si, Gyeonggi-do

first: hoon

last: hur

state: State...

address: 164, World cup-ro, Yeongtong-gu

department: Department of Surgery

country: South Korea

institute: Ajou University

data_processing:
Tophat v2.0.13
cuffdiff v2.2.0
Assembly: human hg19
Supplementary files format and content: One integrated xlsx file includes FPKM for each sample

source_name: gastric cancer

extract_protocol:
Total RNA was extracted from a pair of CAFs and NAFs with RNA extraction reagents (Qiagen).
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).

value: gastric cancer


title: CAF20


title: Covid_female_32220_1_B027_ATAC


title: Covid_female_32038_2_B025_ATAC


title: CAF16


title: Covid_female_32220_2_B027_ATAC


title: Covid_male_31874_1_B025_ATAC


title: NF47

source_name: adjacent normal gastric

value: adjacent normal gastric


title: Diff_rep1_Cu_IgG

value: Primary myoblast cells


title: NF20


title: NF16


title: Healthy_female_11161_1_B025_ATAC

value: female


title: Covid_female_32038_1_B025_ATAC


title: Healthy_female_11404_1_B025_ATAC


title: Covid_male_31874_2_B025_ATAC


title: Healthy_male_11558_1_B025_ATAC


title: Covid_female_32038_3_B025_ATAC

value: Visit 3


title: AR2lane1

description:
GC111201
10X genomics


title: Covid_male_31874_3_B025_ATAC


title: Covid_female_31924_3_B025_ATAC


title: Covid_male_31207_1_B024_ATAC

value: Visit 1


title: Covid_male_31207_4_B024_ATAC


title: Covid_male_31207_2_B024_ATAC

value: Visit 2


title: Covid_female_31924_2_B025_ATAC


title: Covid_male_31207_3_B024_ATAC


title: Covid_female_31924_1_B025_ATAC


title: Healthy_female_11032_1_B033_ATAC


title: Healthy_female_11058_1_B021_ATAC


title: Healthy_female_11004_1_B021_ATAC


title: Healthy_male_11012_1_B011_ATAC


title: Healthy_male_11820_1_B025_ATAC


title: Healthy_male_11261_1_B024_ATAC


title: Healthy_male_11423_1_B011_ATAC


title: Healthy_male_11196_1_B011_ATAC


title: Covid_male_32209_4_B044_RNA


title: Covid_male_42409_3_B044_RNA


title: Covid_male_42409_4_B044_RNA


title: Healthy_male_11219_1_B011_ATAC


title: Healthy_male_11222_1_B011_ATAC


title: Covid_male_32416_4_B044_RNA


title: Covid_female_32054_4_B044_RNA


title: 7D_TCATTG_Input_SW480-Smad4Avi_Birusedforb-catChIP_AP21

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

data_processing:
FastQC (v.0.11.3) was used to check the quality of raw sequencing reads (fastq), and bowtie2 (v.2.2.6) was used to align the sequences to mouse (mm9) or human (hg19) genomes and generate bam files. Deeptools bamCoverage (v.2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files. Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads. The shiftsize parameter used in MACS was based on the fragment size of Pippin Prep. SMAD4 ChIP-seq of SW480 cells are at a P value of 10−5.
Assembly: hg19
Supplementary files format and content: txt file, MACS summit centered peaks

growth_protocol: SW480 cells were cultured in RPMI (Gibco), containing 10% FBS (Gibco) and 1% penicillin and streptomycin (Gibco).

extract_protocol:
Each 100 μl cell pellet was incubated with 1 ml of cross-linking solution containing an equal amount of DSG (Thermo), DSS (Thermo) and EGS (Thermo 21565), creating a final concentration of 2 mM NHS ester (reactive groups). Cells were rocked for 20 min at room temperature, after which fresh formaldehyde was added to make a concentration of 1.22% formaldehyde. The cells were then rocked for an additional 20 min. The cross-linking reaction was stopped with 125 mM glycine. The cells were then washed with PBS, and nuclei were extracted using a Dounce homogenizer and Farnham lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% NP-40, and protease inhibitor cocktails). IP material was subsequently handled as described above for conventional ChIP of sonicated genomic DNA (a final concentration of 0.2% SDS in the sonicates). The diluted sonicates were then incubated with pre-blocked (0.5% BSA/PBS) Streptavidin beads (Invitrogen) overnight at 4°C. The beads were serially washed in low salt (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, and 20 mM HEPES, pH 8.0), high-salt (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X-100, 500 mM NaCl, 1 mM EDTA, and 20 mM HEPES, pH 8.0), LiCl buffer (250 mM LiCl, 0.5% Sodium Deoxycholate, 0.5% NP-40, 1mM EDTA, and 20 mM HEPES, pH 8.0), and a final wash buffer (1 mM EDTA and 20 mM HEPES, pH 8.0). The beads were then incubated at 65 °C for 6 h in reverse cross linking buffer (0.1 mM NaHCO3 and 1% SDS). The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified with PicoGreen (Life Technologies).
5 ng each of ChIP or input DNA was used to prepare ChIP-seq libraries with a Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina).

treatment_protocol: Cells stably expressing both avi-tagged SMAD4 and BirA were selected with medium containing 2 μg/ml puromycin and 0.4 mg/ml Hygromycin B, respectively.

tag: cell line

value: colorectal cancer (CRC)


title: sw480_smad4_bir_TAGCTT.june2015


title: Covid_male_32131_4_B044_RNA


title: Covid_female_32245_4_B044_RNA


title: Mouse_ID_76_DCA-78W

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

data_processing:
Aligned with Bismark v0.14.3 and parameters: -I 15 -X 1000
Methylation quantified with Bismark methylation extractor v0.14.3 and parameter: --no_overlap
Assembly: mm10
Supplementary files format and content: coverage.bigWig: aligned read coverage
Supplementary files format and content: methpct.bigWig: CpG methylation percentages

source_name: liver

growth_protocol: All procedures involving animal care were approved by an EPA Institutional Animal Care and Use Committee. Briefly, mice were received at age 21 days to the EPA AAALAC International accredited facility from Charles River Laboratories in Morrisville, NC, and acclimated for 7 days prior to treatment initiation. The animals were housed in polycarbonate cages in a laminar flow room and maintained under standard conditions (20 ± 2 C°; 40–60% relative humidity; 12 h light/dark cycle) and fed ad libitum Purina 5001 laboratory rodent diet (Purina Test Diets, St. Louis, MO). The study animals

extract_protocol:
Approximately 25 mg of frozen liver tissue was cut on dry ice and immediately placed into a 2 ml vial with ceramic homogenization beads (MP Biomedicals, Lysing Matrix D) containing 360 ul of Qiagen buffer ATL (Qiagen GmbH, Hilden, Germany). The tissue was allowed to equilibrate to room temperature, 20 µl of 40 mg/ml Proteinase K was added and homogenized with a Precellys 24 homogenizer (Bertin Technologies, Villeurbanne, France) at 5500 rpm for 20 s. The homogenized sample tubes were placed in a 56°C thermomixer at gentle agitation for 3 h. After proteinase treatment, the samples were treated with RNAse A, and DNA was isolated using Qiagen’s DNeasy® kit following the manufacturer’s instruction. The isolated DNA was checked for initial purity (A260/280 of ≥ 1.8, A260/230 ≥ 1.0) using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware). Yield was determined by Qubit broad range dsDNA assay kit and protocol (Life Technologies, Carlsbad, CA).
500 ng DNA was digested overnight with MspI (300 ng) or TaqαI (200 ng). Each sample underwent an additional 2 hr digestion before restriction enzyme deactivation. Each restriction enzyme digested DNA sample was pooled and then bead purified using Agencourt Ampure XP beads (Beckman Coulter Life Sciences, Brea, CA), and Qubit quantitation was used to determine the amount of λ for bisulfite methylation efficiency spike-in. End-repair and adapter ligation were performed with the KAPA Hyper Prep kit (Roche, Basle, Switzerland), along with a custom synthesized duplex adapter (Integrated DNA Technologies (IDT), Morrisville, NC). After overnight ligation and subsequent bead cleanup, the samples went through two rounds of bisulfite conversion and clean-up (Qiagen Epitect Bisulfite conversion kit, Germantown, MD). Library amplification was carried out using KAPA HIFI HotStart Uracil+ and IDT synthesized index and universal primer for 12 cycles, followed by bead cleanup. Library quality and yield were determined with the Agilent Bioanalyzer HS DNA kit (Santa Clara, CA), with the library size range predominately between 0 and 600bp. The libraries were sequenced on an Illumina NextSeq (San Diego, CA) by the National Health and Environmental Effect Research Laboratory (NHEERL) Genomics Research Core (GRC) at the US Environmental Protection Agency using the NextSeq 500/500 75 cycle kit.

treatment_protocol: The target dose of 3.5 g/L (429 mg/kg-day) dichloroacetic acid (DCA; CAS 79-43-6, Aldrich, Milwaukee, WI) was based on the earlier carcinogenicity results observed in male mice, and is equivalent to 65 mg/kg-day in humans. The actual dose was estimated based on intake, body weight and water DCA concentrations, and the daily water concentration (ml/kg-day) by cage was measured every 4-5 weeks beginning with week 4. Drinking water stocks were prepared every 12-14 days and checked by ultraviolet absorption at 231nm to confirm DCA concentration (Beckman DU Series 600 spectrophotometer, Beckman Coulter, Brea, CA). The stock water pH was adjusted to 6.8-7.2 with NaOH, stored at 4-6°C and changed every 5-7 days, based on studies showing DCA to be stable over 1-2 weeks. As previously detailed, water consumption was initially 5-22% lower in the DCA drinking water groups, although by 52 weeks, water consumption was equivalent in all groups. The removal of DCA quickly returned water consumption to control levels, regardless of exposure length.

tag: strain

tag: age

value: 4 wks

value: liver

tag: time

value: 78 wks

tag: dose

value: 78 wks DCA


title: Healthy_male_11075_1_B024_ATAC

value: male


title: Covid_female_31945_4_B044_RNA

value: Visit 4


title: Mouse_ID_74_DCA-78W


title: Healthy_female_11096_1_B044_RNA

value: Healthy


title: Mouse_ID_75_DCA-78W


title: Mouse_ID_73_DCA-78W


title: Covid_male_32415_3_B044_RNA


title: Mouse_ID_58_STOP-10WDCA-78WWTR

value: 10 wks 3.5g/L DCA, then 68 wks drinking water


title: Covid_male_32415_4_B044_RNA


title: Mouse_ID_57_STOP-10WDCA-78WWTR


title: Mouse_ID_56_STOP-10WDCA-78WWTR


title: Covid_female_32255_4_B044_RNA


title: DICER1 mutant mouse liver

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

data_processing:
The objectives of smRNA analysis are divided into four following contents.  · Quantification of smRNA expression  · Filtering differentially expressed smRNA  · Prediction of known / novel miRNAs  · Classification by categories of smRNA  1) After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also  trimmed off the raw sequence reads.  2) Both the trimmed reads and non-adapter reads as processed reads are used, to do analyzing long  target (>= 50bp).  3) The processed reads are gathered forming a unique cluster. This cluster contains reads that are 100%  match to the sequence identity as well as read length. The cluster is given its temporary cluster ID  and the number of reads it holds.  4) In order to eliminate the effect of large amounts of rRNA from this study, the read was aligned to the  rRNA sequence and have them removed.  5) rRNA removed reads are sequentially aligned to reference genome, miRBase v22.1 and non-coding  RNA database, RNAcentral 14.0 to classify known miRNAs and other type of RNA such as tRNA, snRNA,  snoRNA etc. Novel miRNA prediction is performed by miRDeep2.  6) The read counts for each smRNA are extracted from mapped smRNAs to report the abundance of each  smRNA.  7) (Optional) Differentially expressed smRNAs are determined through comparing across conditions each  smRNA using statistical methods.
The total number of bases, reads, GC (%), Q20 (%), Q30 (%) are calculated for 3 samples. For  example, in WT, 82,435,935 reads are produced, and total read bases are 4.2Gbp. The GC content (%)  is 53.33% and Q30 is 95.41%.
The reads start at the first base after the 5' sequencing adapter and in Illumina sequencing  typically end after 51 bp (in case of sequencing 51 bp SE). As mature miRNAs are normally up to 25 bp  in length, the reads will contain part of 3' adapter sequence that has to be removed.  Sequenced reads are classified as trimmed reads, non-adapter reads, short reads and low quality  reads according to these criteria. Adapter trimming process is done to eliminate the adapter  sequences that exist in the read using Cutadapt. If a read matches at least first 5 bp of 3' adapter  sequence, it is regarded as an adapter sequence, and then trimmed from the read. Trimmed reads  should be at the minimum of 18 bp in order to be considered reliable for analysis. Afterwards, 3' end  of each read is quality trimmed with -q 10 in Cutadapt. In addition, trimmed or nonAdapter read with  'N' base is regarded as low quality read and filtered.  Here is the definition of four read types describled above.  · Trimmed Read: Read that is removed adapter sequences  · nonAdapter Read: Read that has not adapter sequences  · Short Read: Read with below 17bp in read length after adapter trimming  · Low Quality Read: Read with one or more 'N' base in trimmed or nonAdapter read  In case of analyzing short target (<50bp), the trimmed reads as processed reads are used.  Otherwise, in case of analyzing long target (>= 50bp), both the trimmed reads and non-adapter reads  as processed reads are used.  In this analysis, we analyzed both short target and long target to see comprehensive smRNA  profiles.  For example, a total of 82,435,935 reads were produced from the WT sample, of which 20,756,564  reads included the adapter and the read length after trim was 18bp or more. 42,576,088 reads did not  include the adapter, and 18,904,903 reads were shorter than 18bp after adapter trim.  For the analysis of long targets, 63,332,652 readings are used in the subsequent analysis, including  trimmed reads and nonAdapter reads.
Most of the RNA composition is usually known as rRNA. In order to eliminate the effect of large  amounts of rRNA from this study, reads were aligned to the 45S pre-rRNA and mitochondrial rRNA  of Mus musculus and have them removed.  Figure 6 represents the remaining reads (blue) after removing rRNA (red).  For example a total of 63,332,652 reads left after adapter trimming step from the WT sample, of  which 1,560,403 reads did aligned to rRNA sequences. 61,772,249 reads finally remained in this  filtering step. These reads were used in the following analysis step.
Assembly: mm10
Supplementary files format and content: Txt

source_name: Liver

extract_protocol:
Total RNA of murine liver was prepared using the miRNeasy Mini Kit (Qiagen), according to standard manufacturer’s protocol. Eliminate DNA contamination using DNase.
The small RNA libraries were prepared using SMARTer smRNA-seq kit (Takara Bio.). The single end fragment library (50 bp) was sequenced with the HiSeq2500. The resulting reads were then mapped to the mm10 build of the mouse genome and to miRBase (v22.1) sequence. Read sequences were classified according to the information registered in miRBase to determine whether they were derived from 5p or 3p of Pre-miRNA.

value: Liver

tag: background strain

value: DICER1 mutant


title: Mouse_ID_55_STOP-10WDCA-78WWTR


title: Covid_male_32251_4_B038_RNA


title: Mouse_ID_54_STOP-10WDCA-78WWTR


title: Mouse_ID_53_STOP-10WDCA-78WWTR


title: Covid_female_32196_1_B038_RNA


title: Wild-type mouse liver

value: Wild-type mouse liver


title: Mouse_ID_52_CTRL-78W

value: drinking water only


title: Covid_male_42409_2_B038_RNA


title: Mouse_ID_50_CTRL-78W


title: Covid_male_32415_2_B038_RNA


title: Healthy_male_11872_1_B044_RNA


title: Healthy_male_11160_1_B038_RNA


title: Mouse_ID_49_CTRL-78W


title: Covid_female_32196_3_B038_RNA

value: female


title: Covid_female_32140_4_B044_RNA


title: Covid_male_32416_1_B038_RNA


title: Covid_male_32415_1_B038_RNA


title: cKO, eLPre-B, rep3

city: Kyoto

first: Kotaro

last: Akaki

address: Sakyo-ku, Yoshidakonoecho

department: Department of Medical Chemistry

institute: Kyoto University

data_processing:
BaseSpace Onsite
Acquired data was analyzed using Galaxy 2 (Afgan et al., 2018).
Reads were trimmed using cutadapt 4.0, mapped on the murine genome (mm10) using HISAT2, and counted using featureCounts 2.0.1
Count data was normalized using limma_voom 3.48.0
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: early Lpre-B cell

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen) and isolated with RNA Clean & Concentrator-5 (Zymo Research).
cDNA library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: early Lpre-B cell

value: Upf1 Flox/Flox, Mb1 Cre/+ (cKO)


title: Mouse_ID_47_CTRL-78W


title: cKO, eLPre-B, rep2


title: Covid_male_32416_2_B038_RNA

value: Visit 2


title: Covid_male_42409_1_B038_RNA

value: Visit 1


title: cKO, eLPre-B, rep1


title: Covid_female_32196_2_B038_RNA


title: Healthy_female_11085_1_B038_RNA


title: Ctrl, eLPre-B, rep3

value: Upf1 Flox/Flox, Mb1 +/+ (Control)


title: Covid_female_32220_4_B038_RNA


title: Ctrl, eLPre-B, rep2


title: Covid_female_32124_3_B038_RNA

value: Visit 3


title: Covid_female_32140_3_B038_RNA


title: pUPF1 bound RNA, rep2

data_processing:
BaseSpace Onsite
Acquired data was analyzed using Galaxy 2 (Afgan et al., 2018).
Reads were trimmed using cutadapt, mapped on the murine genome (mm10) using HISAT2, and counted using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: spleen

growth_protocol: RPMI-1640 medium (Nacalai Tesque) supplemented with 10% (vol/vol) FBS (Gibco) and 50 μM b-mercaptoethanol.

extract_protocol:
Cells were lysed and immunoprecipitated with normal rabbit IgG or anti pUPF1 Ab. RNA was harvested using TRIzol reagent (Invitrogen) and isolated with RNA Clean & Concentrator-5 (Zymo Research).
cDNA library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Splenic B cells (CD43- cells) 5 ug/mL of CD40L, 10 ug/mL of anti-IgM antibody, and 20 ng/mL of IL-4 for 72 hours.

value: spleen

tag: group

value: pUPF1 bound RNA

value: B cell

value: Wild type

value: B cell activation


title: pUPF1 bound RNA, rep3


title: pUPF1 bound RNA, rep1


title: normal rabbit IgG bound RNA, rep2

value: normal rabbit IgG bound RNA


title: Covid_female_32255_2_B037_RNA

tag: Sex


title: Covid_male_32209_3_B037_RNA

value: male

tag: visit


title: Covid_female_32245_2_B037_RNA


title: normal rabbit IgG bound RNA, rep3

tag: tissue


title: Mouse_ID_48_CTRL-78W

value: 4 wks

value: liver

value: 78 wks


title: Covid_female_32245_1_B037_RNA

value: female


title: Covid_male_32416_3_B044_RNA


title: Input, rep2

value: Input

tag: cell type


title: Covid_male_32209_1_B037_RNA


title: Input, rep3


title: Covid_male_32209_2_B037_RNA


title: Healthy_female_11534_1_B037_RNA

value: Healthy


title: Mouse_ID_51_CTRL-78W

value: drinking water only


title: normal rabbit IgG bound RNA, rep1


title: Ctrl, eLPre-B, rep1

value: early Lpre-B cell


title: CurLAA_rep3 for PANDORA-seq

city: Guangzhou

first: Xueshan

last: Luo

address: Dongchuan Road

country: China

institute: South China University of Technology

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
SPORTS1.1 (Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs) was used to perfom PANDORA-seq analysis.Junchao Shi, Eun-A Ko, Kenton M. Sanders, Qi Chen, Tong Zhou. SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA-and tRNA-derived small RNAs. Genomics, Proteomics & Bioinformatics (2018) doi.org/10.1016/j.gpb.2018.04.004
Assembly: mm10
Supplementary files format and content: read counts table

source_name: atrial appendages

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.Treatment of RNA with AlkB. The RNA was incubated in 50 μl reaction mixture containing 50mM HEPES (pH 8.0) (Gibco (15630080) and Alfa Aesar (J63578)), 75 μM ferrous ammonium sulfate (pH 5.0), 1 mM α-ketoglutaric acid (Sigma–Aldrich; K1128-25G), 2 mM sodium ascorbate, 50 mg l-1 bovine serum albumin (Sigma–Aldrich; A7906-500G), 4 μg ml-1 AlkB , 2,000 U RNase inhibitor and 200 ng RNA at 37 °C for 30 min. Then, the mixture was added into 500 μl. Treatment of RNA with T4PNK. The RNA was incubated in 50 μl reaction mixture containing 5μl 10× PNK buffer (New England Biolabs; B0201S), 10 mM ATP (New England Biolabs; P0756S), 10 U T4PNK (New England Biolabs; M0201L) and 200 ng RNA at 37 °C for 20 min. Then, the mixture was added into 500 μl TRIzol reagent to perform the RNA isolation procedure.
Small RNA library construction and deep sequencing. The RNA segment was separated by PAGE, then a 15- to 45-nucleotide stripe was selected and recycled. The adapters were obtained from the QIAseq® miRNA Library Kit (QIAGEN: 331505) and ligated sequentially. The amplified flow cell was sequenced using the SE75 strategy on the Illumina system by epibiotek (Guangzhou Epibiotek Co., Ltd., Guangzhou, China)

value: atrial appendages

value: 18 month old

value: with curcumin


title: Covid_female_32245_3_B037_RNA

value: Visit 3


title: CurLAA_rep1 for PANDORA-seq


title: Covid_male_31874_4_B037_RNA

value: Visit 4


title: CurLAA_rep2 for PANDORA-seq

value: 18month old


title: Covid_male_32131_2_B037_RNA

value: Visit 2


title: Covid_female_32255_1_B037_RNA

value: Visit 1


title: 18mLAA_rep3 for PANDORA-seq

value: without curcumin


title: Covid_female_32255_3_B037_RNA


title: 18mLAA_rep2 for PANDORA-seq


title: 5mLAA_rep3 for PANDORA-seq

value: 5 month old


title: Covid_male_32131_3_B037_RNA

value: male


title: Covid_female_32038_5_B037_RNA

value: Visit 5


title: 5mLAA_rep2 for PANDORA-seq


title: 18mLAA_rep1 for PANDORA-seq


title: Covid_male_32131_1_B037_RNA


title: Input, rep1

value: spleen

value: B cell

value: Wild type

value: B cell activation


title: 5mLAA_rep1 for PANDORA-seq


title: Ddis-AX4, 10h, biorep4

city: Gothenburg

first: Bart

last: Edelbroek

address: Medicinaregatan 3B

department: Bioinformatics and Data Centre, Core Facilities

country: Sweden

institute: University of Gothenburg

data_processing:
Adapters trimmed using cutadapt v2.10
Trimmed reads pooled and mapped using STAR v2.7.5
Reads assigned to genes with featureCounts, part of the subread v2.0.1 package
For read mapping and counting, the D_discoideum_PASAua.gff annotation was used from http://dx.doi.org/10.6084/m9.figshare.3384364
Assembly: dicty_2.7 genome assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Dictyostelium discoideum

source_name: 10h developed cells

growth_protocol: D. discoideum AX4 wildtype cells (DictyStockCenter ID: DBS0237637) were grown axenically in HL5-C to exponential phase. 3x10^8 cells were harvested at 400 x g, 5 min, and washed twice in 50 ml KK2

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen), Dnase treated (TURBO Dnase, Invitrogen), Phenol Chloroform purified.
TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection

treatment_protocol: For development, cells were plated on 92mm NN-Agar plates and harvested at the designated time points

value: 10h developed cells

value: grown in HL5-C, developed on NN-Agar plates


title: Covid_female_32220_3_B033_RNA

value: female


title: Healthy_male_11090_1_B037_RNA

value: Healthy


title: Ddis-AX4, 8h, biorep4

source_name: 8h developed cells

value: 8h developed cells


title: Ddis-AX4, 10h, biorep1


title: SC-sriZLC-60h

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

description: 10x Genomics

data_processing:
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis.
Assembly: hg38, mm10

extract_protocol:
Samples were dissociated into single cells and resuspended in 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).


title: Covid_female_31945_3_B033_RNA

value: Visit 3


title: Ddis-AX4, 10h, biorep2


title: Ddis-AX4, 10h, biorep3


title: Ddis-AX4, 8h, biorep2


title: Covid_female_31945_2_B033_RNA


title: SC-hTBLC

description: 10x Genomics


title: Ddis-AX4, 8h, biorep3


title: Ddis-AX4, 8h, biorep1


title: Ddis-AX4, 6h, biorep4

source_name: 6h developed cells

value: 6h developed cells


title: Covid_female_31945_1_B033_RNA


title: Ddis-AX4, 6h, biorep3


title: siSNRPD2_2

description: RNA-seq_wibr3_high_concentration_PlaB_and_siRNA.CSV

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Assembly: hg38

extract_protocol:
RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: hESC

value: WT

value: cultured in E8 medium


title: siSNRPD2_1


title: Ddis-AX4, 6h, biorep2


title: Ddis-AX4, 6h, biorep1


title: Healthy_female_11776_1_B033_RNA

value: Visit 1


title: siNC


title: Ddis-AX4, 4h, biorep4

source_name: 4h developed cells

value: 4h developed cells


title: Healthy_female_11224_1_B033_RNA


title: Ddis-AX4, 4h, biorep2


title: Ddis-AX4, 4h, biorep3


title: WIBR3-10-84h

value: cultured in E8 medium supplemented with 10 nM PlaB


title: Ddis-AX4, 4h, biorep1


title: Healthy_female_11032_1_B033_RNA


title: Covid_male_32251_3_B033_RNA

value: male


title: WIBR3-10-48h


title: Ddis-AX4, 2h, biorep4

source_name: 2h developed cells

value: 2h developed cells


title: Ddis-AX4, 2h, biorep2


title: Ddis-AX4, 2h, biorep3


title: Ddis-AX4, 2h, biorep1


title: Covid_female_32038_4_B033_RNA

source_name: peripheral blood mononuclear cells

value: Visit 4


title: WIBR3-10-72h


title: Ddis-AX4, 0h, biorep3

source_name: vegetative cells

value: vegetative cells

value: grown in HL5-C


title: WIBR3-10-12h


title: Covid_female_32054_3_B027_RNA


title: WIBR3-10-8h


title: Covid_female_32140_2_B027_RNA

value: Visit 2


title: Ddis-AX4, 0h, biorep1


title: WIBR3-10-6h


title: Covid_female_32220_2_B027_RNA

value: female


title: WIBR3-10-4h


title: Covid_female_32054_2_B027_RNA


title: Brain, WT-H4

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
ChIP-seq raw reads were aligned to mouse genome build mm10 using Bowtie2.
Peaks were called using HOMER tools with the following setting: ChIP-seq peak call  threshold (0.001 FDR, with 4 fold enrichment), over IgG control.
Motifs were discovered using HOMER motif analysis function.
Peak annotation was performed to associate peaks with nearest genes using HOMER peak annotation function.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Brain

extract_protocol:
Freshly harvested brain tissues from C57BL/6J mice were enzymatically dissociated with 250 µg/ml papain and 50 µg/ml DNase I in PBS / 2% FBS at 37 oC for 40 minutes. Cell suspension was washed and filtered with 70 µm strainers. After remove the myelin, cells were labeled with CD31-PE and CD45-FTIC antibodies, CD31+CD45- cells were sorted by fluorescence-activated cell sorting (FACS) for ChIP-seq.
Libraries were prepared according to manufacturer's instructions using KAPA DNA HyperPrep Kit (Kapa Biosystems).

value: Brain

value: Brain CD31+CD45- cells

value: Mgpf/f

tag: disease state

value: model of cerebral arteriovenous malformations

tag: chip antibody

value: H4K8ac (ThermoFisher Scientific, Catalog # 710828)


title: Brain, KO-H4


title: WIBR3-10-2h

value: hESC

value: WT


title: Brain, KO-IgG

value: IgG


title: Brain, WT-IgG


title: Ddis-AX4, 0h, biorep4


title: Covid_female_32140_1_B027_RNA

tag: disease

value: Visit 1


title: Brain, WT-H3

tag: genotype

value: H3K27me3 (Abcam, cat# ab6002)


title: Covid_male_32251_1_B027_RNA

value: male


title: Covid_female_32124_2_B027_RNA


title: WIBR3-20-84h

tag: treatment

value: cultured in E8 medium supplemented with 20 nM PlaB


type: genomic

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

description: Genomic DNA from Skeletal Muscle Biopsy_18_204963470085_R02C01_Participant 5_Male_2 Training

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing:
Partek Genomic Suite V7 (Using MethylationEPIC_v-1-0_B4 manifest file)
Data is normalised via functional normalisation (with noob background correction)

label: biotin

source_name: DNA from Vastus Lateralis Muscle_18_204963470085_R02C01_Participant 5_Male_2 Training

label_protocol: Labels (Sample number_Beadchip Barcode_Beadchip position_Participant No_Sex_Condition)

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with  manufacturers guidelines. The DNA was then bisulfite converted using the EZ DNA Methylation Kit, Zymo Research, CA, United States, as per manufacturer’s instructions.

value: Male

value: Skeletal Muscle_Vastus Lateralis

tag: timepoint

value: Training


description: Genomic DNA from Skeletal Muscle Biopsy_16_204963470068_R08C01_Participant 4_Female_4 Retraining

source_name: DNA from Vastus Lateralis Muscle_16_204963470068_R08C01_Participant 4_Female_4 Retraining

value: Female

value: Retraining


description: Genomic DNA from Skeletal Muscle Biopsy_19_204963470085_R03C01_Participant 5_Male_3 Detraining

source_name: DNA from Vastus Lateralis Muscle_19_204963470085_R03C01_Participant 5_Male_3 Detraining

value: Detraining


title: WIBR3-20-72h

tag: cell line


description: Genomic DNA from Skeletal Muscle Biopsy_15_204963470068_R07C01_Participant 4_Female_3 Detraining

source_name: DNA from Vastus Lateralis Muscle_15_204963470068_R07C01_Participant 4_Female_3 Detraining


description: Genomic DNA from Skeletal Muscle Biopsy_20_204963470085_R04C01_Participant 5_Male_4 Retraining

source_name: DNA from Vastus Lateralis Muscle_20_204963470085_R04C01_Participant 5_Male_4 Retraining


description: Genomic DNA from Skeletal Muscle Biopsy_17_204963470085_R01C01_Participant 5_Male_1 Baseline

source_name: DNA from Vastus Lateralis Muscle_17_204963470085_R01C01_Participant 5_Male_1 Baseline

value: Baseline


title: Covid_male_32251_2_B027_RNA

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Genome_build: Ensembl GRCh38-3.0.0
Supplementary_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

extract_protocol:
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

value: Visit 2


title: Ddis-AX4, 0h, biorep2

value: vegetative cells

value: grown in HL5-C


title: WIBR3-20-48h

value: hESC


description: Genomic DNA from Skeletal Muscle Biopsy_14_204963470068_R06C01_Participant 4_Female_2 Training

source_name: DNA from Vastus Lateralis Muscle_14_204963470068_R06C01_Participant 4_Female_2 Training


description: Genomic DNA from Skeletal Muscle Biopsy_13_204963470068_R05C01_Participant 4_Female_1 Baseline

source_name: DNA from Vastus Lateralis Muscle_13_204963470068_R05C01_Participant 4_Female_1 Baseline


title: Brain, KO-H3

value: Brain

tag: strain

value: Brain CD31+CD45- cells

value: model of cerebral arteriovenous malformations


title: WIBR3-20-24h

value: WT


description: Genomic DNA from Skeletal Muscle Biopsy_12_204963470068_R04C01_Participant 3_Male_4 Retraining

source_name: DNA from Vastus Lateralis Muscle_12_204963470068_R04C01_Participant 3_Male_4 Retraining


description: Genomic DNA from Skeletal Muscle Biopsy_11_204963470068_R03C01_Participant 3_Male_3 Detraining

source_name: DNA from Vastus Lateralis Muscle_11_204963470068_R03C01_Participant 3_Male_3 Detraining


title: Covid_female_32124_1_B027_RNA

value: female

value: Visit 1


title: WIBR3-10-1h

value: cultured in E8 medium supplemented with 10 nM PlaB


title: WIBR3-20-12h

value: cultured in E8 medium supplemented with 20 nM PlaB


description: Genomic DNA from Skeletal Muscle Biopsy_10_204963470068_R02C01_Participant 3_Male_2 Training

source_name: DNA from Vastus Lateralis Muscle_10_204963470068_R02C01_Participant 3_Male_2 Training

value: Male

value: Skeletal Muscle_Vastus Lateralis

value: Training


description: Genomic DNA from Skeletal Muscle Biopsy_9_204963470068_R01C01_Participant 3_Male_1 Baseline

source_name: DNA from Vastus Lateralis Muscle_9_204963470068_R01C01_Participant 3_Male_1 Baseline


title: Covid_female_32220_1_B027_RNA


description: Genomic DNA from Skeletal Muscle Biopsy_8_204963470004_R08C01_Participant 2_Male_4 Retraining

source_name: DNA from Vastus Lateralis Muscle_8_204963470004_R08C01_Participant 2_Male_4 Retraining

value: Retraining


title: WIBR3-20-8h


title: Covid_female_32038_2_B025_RNA


description: Genomic DNA from Skeletal Muscle Biopsy_7_204963470004_R07C01_Participant 2_Male_3 Detraining

source_name: DNA from Vastus Lateralis Muscle_7_204963470004_R07C01_Participant 2_Male_3 Detraining

value: Detraining


description: Genomic DNA from Skeletal Muscle Biopsy_6_204963470004_R06C01_Participant 2_Male_2 Training

source_name: DNA from Vastus Lateralis Muscle_6_204963470004_R06C01_Participant 2_Male_2 Training


title: WIBR3-20-6h


title: Covid_male_31874_1_B025_RNA

source_name: peripheral blood mononuclear cells

value: male


description: Genomic DNA from Skeletal Muscle Biopsy_2_204963470004_R02C01_Participant 1_Male_2 Training

source_name: DNA from Vastus Lateralis Muscle_2_204963470004_R02C01_Participant 1_Male_2 Training


description: Genomic DNA from Skeletal Muscle Biopsy_5_204963470004_R05C01_Participant 2_Male_1 Baseline

source_name: DNA from Vastus Lateralis Muscle_5_204963470004_R05C01_Participant 2_Male_1 Baseline

value: Baseline


title: WIBR3-20-2h

description: RNA-seq_wibr3_high_concentration_PlaB_and_siRNA.CSV


description: Genomic DNA from Skeletal Muscle Biopsy_3_204963470004_R03C01_Participant 1_Male_3 Detraining

source_name: DNA from Vastus Lateralis Muscle_3_204963470004_R03C01_Participant 1_Male_3 Detraining


title: Covid_female_32054_1_B027_RNA


description: Genomic DNA from Skeletal Muscle Biopsy_1_204963470004_R01C01_Participant 1_Male_1 Baseline

source_name: DNA from Vastus Lateralis Muscle_1_204963470004_R01C01_Participant 1_Male_1 Baseline


title: Healthy_female_11161_1_B025_RNA

value: Healthy


title: WIBR3-20-1h

value: hESC


title: IPS18-E-MYCP-P6-rep

value: iPSC

value: cultured in E-MYCP medium


title: Healthy_female_11404_1_B025_RNA


title: Covid_female_32038_1_B025_RNA


title: WIBR3-E-MYCP-INTER-P4


title: Covid_male_31874_2_B025_RNA

value: Visit 2


description: Genomic DNA from Skeletal Muscle Biopsy_4_204963470004_R04C01_Participant 1_Male_4 Retraining

source_name: DNA from Vastus Lateralis Muscle_4_204963470004_R04C01_Participant 1_Male_4 Retraining


title: WIBR3-E-MYCP-INTER-P3

value: WT


title: Donor_12_Fetal_23w4d_NR_GEX

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: Multiome_23w4d_NR_filtered_feature_bc_matrix.h5

data_processing:
The fastq files from the scRNA-seq and scATAC-seq libraries from each sample were processed into a single raw count matrix with both gene expression and ATAC peak counts using Cell Ranger arc v2.0.0. raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol,genomic coordinates; raw_matrix_background_barcodes_included:False
Assembly: GRCh38
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI,fragment ends
Supplementary files format and content: fragments_file_format:tsv, fragments_file_content:per unique fragment information, fragments_file_tbi_content:fragment index

source_name: peripheral region of retina

extract_protocol:
The human samples from PCW 10 to PCW 23 were collected from 12 individuals in this study from the UC Davis Eye Center. All the samples were collected within 6 hours post-mortem. The macula and peripheral retina samples were collected with a 2mm disposable biopsy punch and flash-frozen by liquid nitrogen. Samples were then stored at -80_C Nuclei were isolated by Wheaton Dounce Tissue Grinder in pre-chilled fresh-made RNase-free lysis buffer.
The snRNA-seq and snATAC-seq libraries were prepared with Chromium Next GEM Single Cell Multiome GEM kit (10x Genomics) following the manufacturer’s protocols.
scRNA-Seq, scATAC-Seq

value: peripheral region of retina

tag: assay

value: 10x multiome-GEX-v1

value: not determined

tag: ethnicity

value: Unknown

tag: age

value: 165 days (post-conception)

tag: donor id

tag: rawmatrix cellranger_assay_chemistry

tag: rawmatrix assays

value: snATAC-seq,snRNA-seq


title: Donor_11_Fetal_23w1d_NR_GEX

description: Multi_Fetal_23w1d_NR_filtered_feature_bc_matrix.h5

tag: Sex

value: 162 days (post-conception)


title: Donor_1_Fetal_10w_FR_GEX

description: Multiome_10w_FR_filtered_feature_bc_matrix.h5

source_name: macula lutea

tag: tissue

value: macula lutea

value: 70 days (post-conception)

value: snRNA-seq,snATAC-seq


title: WIBR3-20-4h

tag: cell type

value: cultured in E8 medium supplemented with 20 nM PlaB


title: Covid_female_31924_1_B025_RNA

value: female

tag: visit

value: Visit 1


title: Donor_11_Fetal_23w1d_NR_ATAC

library_source: genomic single cell

value: 10x multiome-ATAC-v1


title: Donor_12_Fetal_23w4d_FR_ATAC

description: Multiome_23w4d_FR_filtered_feature_bc_matrix.h5


title: Donor_12_Fetal_23w4d_NR_ATAC


title: Donor_4_Fetal_13W_FR_ATAC

description: Multi_Fetal_13W_FR_filtered_feature_bc_matrix.h5

value: 91 days (post-conception)


title: Healthy_male_11820_1_B025_RNA

value: Healthy

value: male


title: Donor_1_Fetal_10w_FR_ATAC


title: WIBR3-E-MYCP-P1

value: hESC

value: WT

value: cultured in E-MYCP medium


title: Donor_8_Fetal_19W4d_NR_ATAC

description: Multi_Fetal_19W4d_NR_filtered_feature_bc_matrix.h5

value: peripheral region of retina

value: not determined

value: Unknown

value: 137 days (post-conception)


title: Donor_8_Fetal_19W4d_NR_GEX

value: 10x multiome-GEX-v1

value: snATAC-seq,snRNA-seq


title: WIBR3-E-MYCP-P2


title: Covid_female_31924_2_B025_RNA

value: Visit 2


title: Healthy_male_11558_1_B025_RNA


title: Donor_4_Fetal_13W_FR_GEX

value: macula lutea


title: Donor_9_Fetal_20w1d_NR_ATAC

description: Multiome_20w1d_NR_filtered_feature_bc_matrix.h5

value: 141 days (post-conception)


title: Covid_female_32038_3_B025_RNA

value: female

value: Visit 3


title: Donor_9_Fetal_20w1d_NR_GEX


title: ATAC-Primed

data_processing:
ATAC-seq data are processed used the ATAC-seq pipeline from Kundaje lab with auto-detected adapter mode to trim the reads.
Bowtie2 was used to align the reads to genome sequence and Picard was used to remove duplicates and we only remained the high-quality reads.
Peaks are calling by MACS2.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
50,000 living cells were collected in a tube, centrifuged at 500 g at 4°C.
ATAC-seq was performed as the previously described method (Corces et al., 2017) with some   modification.


title: Donor_3_Fetal_12w3d_NR_ATAC

description: Multiome_12w3d_NR_filtered_feature_bc_matrix.h5

value: 10x multiome-ATAC-v1

value: 87 days (post-conception)


title: Donor_3_Fetal_12w3d_NR_GEX


title: Covid_male_31874_3_B025_RNA

value: male


title: Donor_12_Fetal_23w4d_FR_GEX

value: 165 days (post-conception)


title: ATAC-hTBLC

value: hESC


title: SC-Naïve-33h

description: 10x Genomics


title: SC-Naïve-41h

description: 10x Genomics


title: Donor_2_Fetal_11w2d_FR_GEX

description: Multi_Fetal_11w2d_FR_filtered_feature_bc_matrix.h5

value: 79 days (post-conception)


title: Covid_male_31207_1_B024_RNA

value: Visit 1


title: Donor_3_Fetal_12w3d_FR_ATAC

description: Multiome_12w3d_FR_filtered_feature_bc_matrix.h5

value: not determined


title: Covid_male_31207_3_B024_RNA


title: Donor_11_Fetal_23w1d_FR_GEX

description: Multi_Fetal_23w1d_FR_filtered_feature_bc_matrix.h5

value: Unknown

value: 162 days (post-conception)


title: SC-blastoid

description: 10x Genomics


title: Covid_male_31207_4_B024_RNA

value: Visit 4


title: Donor_11_Fetal_23w1d_FR_ATAC

value: snATAC-seq,snRNA-seq


title: Donor_2_Fetal_11w2d_FR_ATAC


title: Donor_10_Fetal_20W2d_FR_ATAC

description: Multi_Fetal_20W2d_FR_filtered_feature_bc_matrix.h5

value: 142 days (post-conception)


title: Donor_1_Fetal_10w_NR_ATAC

description: Multiome_10w_NR_filtered_feature_bc_matrix.h5

value: peripheral region of retina

value: 70 days (post-conception)


title: Donor_10_Fetal_20W2d_FR_GEX

value: macula lutea

value: 10x multiome-GEX-v1


title: SC-teratoma-hTBLC

description: 10x Genomics

source_name: teratoma

value: teratoma


title: Healthy_male_11075_1_B024_RNA

value: Healthy


title: Donor_5_Fetal_14w2d_NR_GEX

description: Multiome_14w2d_NR_filtered_feature_bc_matrix.h5

value: 100 days (post-conception)


title: Donor_5_Fetal_14w2d_NR_ATAC

value: 10x multiome-ATAC-v1


title: Covid_female_31924_3_B025_RNA

value: female

value: Visit 3


title: SC-Naïve-77h

description: 10x Genomics

value: hESC


title: SC-teratoma-Primed

description: 10x Genomics


title: Donor_1_Fetal_10w_NR_GEX

value: not determined


title: Donor_9_Fetal_20w1d_FR_ATAC

description: Multiome_20w1d_FR_filtered_feature_bc_matrix.h5

value: Unknown

value: 141 days (post-conception)

value: snRNA-seq,snATAC-seq


title: Donor_3_Fetal_12w3d_FR_GEX

value: 87 days (post-conception)

value: snATAC-seq,snRNA-seq


title: SC-Naïve-0h

description: 10x Genomics


title: Covid_male_31207_2_B024_RNA

value: male

value: Visit 2


title: Healthy_male_11261_1_B024_RNA

value: Visit 1


title: SC-E8-r104h

description: 10x Genomics


title: Donor_9_Fetal_20w1d_FR_GEX

value: macula lutea

value: 10x multiome-GEX-v1


title: Donor_5_Fetal_14w2d_FR_GEX

description: Multiome_14w2d_FR_filtered_feature_bc_matrix.h5


title: Donor_5_Fetal_14w2d_FR_ATAC


title: Donor_10_Fetal_20W2d_NR_GEX

description: Multi_Fetal_20W2d_NR_filtered_feature_bc_matrix.h5

value: peripheral region of retina

value: 142 days (post-conception)


title: SC-E8-r56h

description: 10x Genomics


title: SC-E8-r36h

description: 10x Genomics


title: Donor_8_Fetal_19W4d_FR_ATAC

description: Multi_Fetal_19W4d_FR_filtered_feature_bc_matrix.h5

value: 10x multiome-ATAC-v1

value: 137 days (post-conception)


title: Donor_10_Fetal_20W2d_NR_ATAC


title: Healthy_male_11012_1_B011_RNA

value: Healthy


title: Healthy_male_11423_1_B011_RNA


title: Donor_7_Fetal_16w4d_FR_GEX

description: Multiome_16w4d_FR_filtered_feature_bc_matrix.h5

value: 116 days (post-conception)


title: SC-E8-r6h

description: 10x Genomics

value: hESC


title: Donor_7_Fetal_16w4d_FR_ATAC

value: not determined

value: Unknown


title: Donor_2_Fetal_11w2d_FR_2_GEX

description: Multi_Fetal_11w2d_FR_2_filtered_feature_bc_matrix.h5

value: 79 days (post-conception)


title: H3K27me3-hTBLC

data_processing:
ChIP-seq reads were trimmed by Trimmomatic software
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie. The duplicates were removed by samtools markdup command
Peaks were called uing MACS v2.1.4, differential peaks were detected by macs2 bdgdiff.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme).

value: hTBLC

tag: chip antibody

value: H3K27me3 (Cell Signaling, #9733T)


title: Donor_2_Fetal_11w2d_FR_2_ATAC

value: snATAC-seq,snRNA-seq


title: Healthy_male_11222_1_B011_RNA

tag: disease

value: male


title: Healthy_female_11058_1_B021_RNA

value: female

value: Visit 1


title: Donor_7_Fetal_16w4d_NR_ATAC

description: Multiome_16w4d_NR_filtered_feature_bc_matrix.h5


title: Donor_7_Fetal_16w4d_NR_GEX

value: 10x multiome-GEX-v1


title: H3K27me3-Primed


title: Healthy_female_11004_1_B021_RNA


title: Donor_6_Fetal_14w5d_FR_ATAC

description: Multi_Fetal_14w5d_FR_filtered_feature_bc_matrix.h5

value: macula lutea

value: 103 days (post-conception)


title: Healthy_male_11196_1_B011_RNA


title: H3K4me3-hTBLC

value: H3K4me3 (Abcam, #ab8580)


title: H3K4me3-Primed


title: SC-E8-r12h

description: 10x Genomics


title: Donor_4_Fetal_13W_NR_GEX

description: Multi_Fetal_13W_NR_filtered_feature_bc_matrix.h5

value: peripheral region of retina

value: 91 days (post-conception)

value: snRNA-seq,snATAC-seq


title: Healthy_male_11003_1_B011_RNA

value: Healthy


title: Donor_4_Fetal_13W_NR_ATAC

value: 10x multiome-ATAC-v1

value: not determined


title: Donor_6_Fetal_14w5d_NR_GEX

description: Multi_Fetal_14w5d_NR_filtered_feature_bc_matrix.h5

value: Unknown


title: Donor_6_Fetal_14w5d_NR_ATAC


title: IPS18-E-MYCP-P10-rep

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Assembly: hg38
Supplementary files format and content: Data were normalized by total mapped reads of each library (CPM: count per million).

value: IPSC

tag: genotype

value: WT

value: cultured in E-MYCP medium

tag: time


title: Donor_2_Fetal_11w2d_NR_ATAC

description: Multi_Fetal_11w2d_NR_filtered_feature_bc_matrix.h5

value: 79 days (post-conception)


title: Donor_2_Fetal_11w2d_NR_GEX


title: FaDu shBACh1 cells, 6 hours HGF treatment

city: Washington

first: Kennedy

middle: Davis

last: Brock

state: DC

address: 2300 I St NW Rm 437, Ross Hall

department: Biochemistry

institute: George Washington University

data_processing:
Bioinformatic analysis was outsourced to Theragen Bio
Assembly: GRCh38.p13
Supplementary files format and content: Excel file includes raw read count, RPKM, and TPM for each sample by gene
Supplementary files format and content: Excel file includes raw read count, RPKM, and TPM for each sample by transcript

source_name: FaDu

growth_protocol: All cells were grown in MEM media supplemented with antibiotics-antimycotics and 10% fetal bovine serum

extract_protocol:
RNA was extracted from TRIzol using manufacturer's protocol
TruSeq Stranded mRNA

treatment_protocol: Cells were treated for 0, 3, or 6 hours with 30ng per mL recombinant human HGF

value: FaDu

value: HNSCC tumor cells

tag: treatment

value: HGF treatment - 6 hours


title: IPS18-E-MYCP-P8

tag: cell line


title: FaDu shBACH1 cells, 3 hours HGF treatment

value: HGF treatment - 3 hours


title: FaDu shBACH1 cells, untreated

value: control


title: Donor_6_Fetal_14w5d_FR_GEX

value: macula lutea

value: 10x multiome-GEX-v1

value: 103 days (post-conception)

value: snATAC-seq,snRNA-seq


title: FaDu shControl cells, 6 hours HGF treatment

value: shControl


title: Healthy_male_11219_1_B011_RNA

value: Healthy

value: male

value: Visit 1


title: FaDu shControl cells, untreated


title: Donor_8_Fetal_19W4d_FR_GEX

value: not determined

value: Unknown

value: 137 days (post-conception)


title: IPS18-E-MYCP-P6

value: IPSC

value: WT

value: cultured in E-MYCP medium


title: IPS18-E8

value: cultured in E8 medium


title: Detroit562 shBACh1 cells, 6 hours HGF treatment

value: HNSCC tumor cells

value: HGF treatment - 6 hours


title: FaDu shControl cells, 3 hours HGF treatment

value: FaDu

value: HGF treatment - 3 hours


title: IPS18-E-MYCP-P2


title: IPS18-E8-rep


title: WIBR3-50-84h

description: RNA-seq_wibr3_high_concentration_PlaB.CSV

value: hESC

value: cultured in E8 medium supplemented with 50 nM PlaB


title: Detroit562 shControl cells, 6 hours HGF treatment

value: shControl


title: WIBR3-50-72h


title: MRC5_siELN_day4 Replicate 3

type: RNA

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2  Microarrays (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Whole Human Genome Microarrays 4x44K v2 (Agilent Technologies)  were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized to the 75th percentile signal intensity and the baseline was adjusted on control condition siCTRL using GeneSpring GX 12.6 software (Agilent Technologies). Numbers are Log2 expression relative to control condition

source_name: MRC5 fibroblast 4 days after siELN transfection

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MRC5 normal human fibroblasts (ATCC) were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Life Technologies) with GlutaMax and supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin/streptomycin (ThermoFisher Scientific). Cells were maintained at 37°C under a 5% CO2 atmosphere. All experiments were carried out on cells at early passages (between 22 and 28).

extract_protocol: Total RNA was extracted from MRC5 cells 1 day or 4 days after siRNA transfection using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

treatment_protocol: MRC5 cells were transfected with siRNA pool (Horizon Discovery) with ON-Targetplus SMART pools of 4 siRNA targeting ELN gene (siELN) or non-targeting siRNA pool as control (siCTRL)

value: siELN transfection

value: 4 days


title: MRC5_siCTRL_R3

source_name: MRC5 fibroblast 4 days after siCTRL transfection

value: siCTRL transfection


title: MRC5_siELN_day1 Replicate 3

source_name: MRC5 fibroblast 1 days after siELN transfection

value: 1 days


title: MRC5_siELN_day4 Replicate 1


title: MRC5_siELN_day4 Replicate 2


title: MRC5_siELN_day1 Replicate 1


title: GFP-Z-3

city: Shanghai

last: Wan

state: Shanghai

address: 300 Feng Lin Road

department: CAS Center for Excellence in Molecular Plant Sciences

institute: Chinese Academy of Sciences

data_processing:
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality.
These clean data were further mapped to pre-defined reference genome generating mapped data.
Assessment on insert size and sequencing randomness were processed on mapped data as library quality control.
Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization.
Assembly: Nicotiana benthamiana draft genome sequence v1.0.1
Supplementary files format and content: Annotation and read counts for every RNA and every sample in txt format.

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: Nicotiana benthamiana was planted in the greenhouse (16-h-light/8-h-dark photoperiod) at 25°C.

extract_protocol:
Total RNA was extracted using Trizol reagent.
(1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

treatment_protocol: Nicotiana benthamiana plants were infiltrated with Agrobacterium harboring plasmid 35S-NlCSP11, 35S-XopQ and 35S-GFP, respectively. The samples consisted of six groups. Two experimental groups include N. benthamiana leaves infiltrated with NlCSP11 (NlCSP11_Z) and the upper uninfiltrated leaves (NlCSP11_U). The four control groups include the infiltrated leaves (XopQ_Z, GFP_Z) and the upper uninfiltrated leaves (XopQ_U, GFP_U).

value: leaves

value: tissue

value: treatment

value: GFP infiltrated leaves


title: WIBR3-50-48h

value: WT


title: GFP-U-3

value: The upper uninfiltrated leaves of GFP-infiltrated Nicotiana benthamiana


title: GFP-U-1


title: HDF, wound exudate WE43, replicate 3

city: Vienna

first: Barbara

last: Wolff-Winiski

state: Other (Non US)

address: Dr. Bohr-Gasse 7

country: Austria

institute: Akribes Biomedical

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) version 1.18.66.3
BCL files were converted to bam files with bcl2fastq VN:2.20.0
Adapters are clipped with trimgalore (Trim Galore!) (Martin 2011)
Abundant sequence fractions (rRNA) are removed using (bowtie2) (Langmead and Salzberg 2012)
Cleaned raw reads are mapped against the reference genome (hg38, iGenomes) with STAR (reverse_stranded, STAR) (Dobin et al. 2013).
Mapped reads are assigned to corresponding genes using featureCounts (featureCounts) (Liao, Smyth, and Shi 2014).
Abundances are estimated through Kallisto Kallisto) (Bray, Pimentel, and Pachter 2016) and Salmon (Salmon against the transcriptome (Patro R 2017).
Assembly: hg38, iGenomes
Supplementary files format and content: Tab delimited text files with the title "NS79-2019_featurecounts.count.gene_Med-WE.txt" contain raw counts for all samples
Supplementary files format and content: Tab delimited text files with the title "NS79-2019_featurecounts.cpm.gene_Med-WE.txt" contain normalized values (counts per million) for all samples

source_name: skin

growth_protocol: HDFs (passage 5-15), pre-seeded at 1x10e5 cells/well in 24-well plates for 24 hours, were incubated for 6h with medium +/- non-healing WE from three different human donors at concentrations that reduced fibroblast proliferation to 30% of control cells after 72h. Cells were incubated at 37°C in humidified 5% CO2/air.

extract_protocol:
Total RNA isolation was performed using the RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s recommendation. RNA quantification and quality control was performed using a Fragment Analyzer 5300 (Agilent).
500 ng of high-quality RNA were used to generate sequencing libraries using the SENSE mRNA-Seq Lib Prep Kit V2 (Lexogen) following the manufacturer’s recommendation. The libraries underwent quality control by Fragment Analyzer and RT-PCR (Library Quant Kit KK4827, Roche)

treatment_protocol: For medium control, cells were cultured in low glucose DMEM medium supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/100 µg/ml streptomycin, and 2 mM glutamine. For wound exudates treatment, wound exudates were diluted in supplemented medium to the desired concentration and sterile-filtered.

value: skin

value: primary human dermal fibroblasts (HDF) (pools of 5 juvenile donors)

value: wound exudate from mixed arterial/venous leg ulcer


title: GFP-U-2


title: MRC5_siELN_day1 Replicate 2


title: Detroit562shControl cells, 3 hours HGF treatment

value: HNSCC tumor cells

value: HGF treatment - 3 hours


title: Detroit562 shBACH1 cells, 3 hours HGF treatment


title: GFP-Z-2


title: WIBR3-50-24h

value: hESC

value: cultured in E8 medium supplemented with 50 nM PlaB


title: GFP-Z-1


title: Detroit562 shControl cells, untreated

value: shControl

value: control


title: HDF, wound exudate WE43, replicate 2


title: MRC5_siCTRL_R1

value: siCTRL transfection

value: 4 days


title: Detroit562 shBACH1 cells, untreated


title: WIBR3-50-12h


title: Cal27 shBACh1 cells, 6 hours HGF treatment

value: HGF treatment - 6 hours


title: HDF, wound exudate WE43, replicate 1


title: WIBR3-50-8h


title: MRC5_siCTRL_R2


title: XopQ-U-3

value: leaves

value: tissue

value: The upper uninfiltrated leaves of XopQ-infiltrated Nicotiana benthamiana


title: WIBR3-50-6h

value: WT


title: XopQ-U-2

value: treatment


title: HDF, wound exudate WE78, replicate 2

value: skin

value: wound exudate from trauma/surgery wound


title: Cal27 shBACH1 cells, 3 hours HGF treatment


title: Cal27 shControl cells, 3 hours HGF treatment


title: HDF, wound exudate WE78, replicate 1

value: primary human dermal fibroblasts (HDF) (pools of 5 juvenile donors)


title: HDF, wound exudate WE78, replicate 3


title: HDF, medium control, replicate 3

value: medium control


title: XopQ-U-1


title: CSP11-U-2

value: The upper uninfiltrated leaves of NlCSP11-infiltrated Nicotiana benthamiana


title: Cal27 shControl cells, untreated

value: HNSCC tumor cells


title: Cal27 shBACH1 cells, untreated


title: WIBR3-50-2h

value: hESC

value: cultured in E8 medium supplemented with 50 nM PlaB


title: HDF, medium control, replicate 2


title: CSP11-U-3


title: WIBR3-50-4h


title: HDF, medium control, replicate 1


title: XopQ-Z-3

value: XopQ infiltrated leaves


title: WIBR3-50-1h


title: EB-Primed-D15

description: RNA-seq_primed_wibr3_differentiation.CSV

value: cultured in E6 medium


title: CSKN_POS17C6

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Hisat2 (version 2.2.1)
SAMtools (version 1.1.4)
stringtie (version 2.1.7)
Bioconductor package DESeq2
Assembly: hg38
Supplementary files format and content: csv format, gene expression levels (normalized reaad counts from the DEseq2 package) for each sample

source_name: hiPSC derived excitatory neurons

growth_protocol: Neural maturation medium (Neurobasal medium A (Gibco, Grand Island, NY, USA),

extract_protocol:
Quick-RNA MiniPrep Kit (Zymo Research #R1054)
e 250~300 bp insert , strand-specific libraries with rRNA removal.
Fragmentation, Reverse Transcription, Second strand cDNA synthesis, End repair and A-tailing, , adapter ligation, Size selection, PCR amplification

value: hiPSC derived excitatory neurons

value: edited


title: CSKN_POS17C5


title: HDF, wound exudate WE224, replicate 3

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) version 1.18.66.3
BCL files were converted to bam files with bcl2fastq VN:2.20.0
Adapters are clipped with trimgalore (Trim Galore!) (Martin 2011)
Abundant sequence fractions (rRNA) are removed using (bowtie2) (Langmead and Salzberg 2012)
Cleaned raw reads are mapped against the reference genome (hg38, iGenomes) with STAR (reverse_stranded, STAR) (Dobin et al. 2013).
Mapped reads are assigned to corresponding genes using featureCounts (featureCounts) (Liao, Smyth, and Shi 2014).
Abundances are estimated through Kallisto Kallisto) (Bray, Pimentel, and Pachter 2016) and Salmon (Salmon against the transcriptome (Patro R 2017).
Assembly: hg38, iGenomes
Supplementary files format and content: Tab delimited text files with the title "NS18-2020_featurecounts.count.gene_Med-WE224.txt" contain raw counts for all samples
Supplementary files format and content: Tab delimited text files with the title "NS18-2020_featurecounts.cpm.gene_Med-WE224.txt" contain normalized values (counts per million) for all samples

value: wound exudate from diabetic foot ulcer


title: XopQ-Z-2

value: leaves

value: tissue


title: EB-Primed-D12

value: WT


title: CSKN_POS17C4


title: HDF, wound exudate WE224, replicate 2


title: XopQ-Z-1

value: treatment


title: CSP11-U-1


title: CSKN_POS_M


title: EB-Primed-D8


title: CSKN_NEG_RW

value: not edited


title: HDF, medium control, replicate 3

value: skin


title: Cal27 shControl cells, 6 hours HGF treatment

value: shControl

value: HGF treatment - 6 hours


title: CSP11-Z-1

value: NlCSP11 infiltrated leaves


title: CSP11-Z-3


title: HDF, medium control, replicate 2

value: primary human dermal fibroblasts (HDF) (pools of 5 juvenile donors)

value: medium control


title: EB-Primed-D5

value: hESC


title: HDF, medium control, replicate 1


title: CSKN_POS_11


title: EB-Primed-D2


title: WIBR3-50-0h

value: cultured in E8 medium


title: EB-hTBLC-D12

value: cultured in E6 medium


title: CSKN_NEG_19

value: hiPSC derived excitatory neurons


title: YY1_Cut&Run_LPKO_Vector_LCL_Rep3

city: Durham

first: Jana

last: Cable

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Aligned to hg38/EBV concatenated genome using Nextflow nf-core/cutandrun
Bam files were sorted (samtools) and converted to bedgraph files
Peaks were called using SEACR with IgG as background, and settings "norm" and "relaxed"
Bedgraph files were normalized by read depth and converted to bigwig files (bedGraphtoBigWig)
Assembly: hg38+NC007605
Supplementary files format and content: Bed files contain peaks called by SEACR using IgG as background control
Supplementary files format and content: Bigwig files contain normalized YY1 Cut&Run reads
Library strategy: Cut&Run

source_name: LCL

extract_protocol:
Cut&Run was performed following kit protocol (Epicypher 14-1048) with a 1 min, 1% formaldehyde fixation
Libraries were prepared using the CUTANA CUT&RUN Library prep kit (Epicyhper 14-1001) according to protocol instructions with modifications. End repeat was modified to 20C for 20 minutes followed by 50C for 1 hour. PCR clean up beads (CNGS-0001) were used at 1.25x after ligation and 1.1x after indexing PCR to enrich for smaller fragments.

tag: donor

value: LCL

tag: cut&run antibody

value: YY1 (CST, D5D9Z)

value: LPKO

value: Vector


title: E15.5 Upf2fl/fl Emx1-Cre+ mouse cortex

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside

description:
KO
10x Genomics

data_processing:
STAR (version 2.7.11a, reference genome: mm10-2020-A<based on Gencode vM23, and filtering out pseudogenes, TEC, miRNA etc. a total of 32285 genes) was used to perform alignment, filtering, barcode counting, and UMI counting for single cell RNA-Seq.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
The E15.5 embryonic cortex tissues were dissected out and transferred to a new 15 ml conical tube along with HEB medium (Hibernate A medium containing 1x B27 and 1x GlutaMAX) to cover the tissues. The nuclei isolation was performed according to the 10x Genomics protocol (CG000124). In brief, tissue was incubated on ice in 3 ml chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% Nonidet P40 Substitute) for 4 minutes. Then, 3 ml chilled HEB medium was added to the lysed cells and mixed with the fire polished silanized Pasteur pipette for around 20 passes. 30 µm MACS SmartStrainer was used to remove cell debris and large clumps. Next, we centrifuged at 500 rcf for 5 min at 4ºC and removed the supernatant without disrupting the nuclei pellet. 3 ml Nuclei Wash and Resuspension Buffer (1x PBS with 1.0% BSA and 0.2 U/µl RNase inhibitor) was used twice to wash the isolated nuclei. Finally, we centrifuged at 500 rcf for 5 min at 4ºC and resuspended in Nuclei Wash and Resuspension Buffer to a final concentration of 1200 nuclei per µl in WT and 900 nuclei per µl in Emx1-Upf2cKO.
Single nuclei were loading the single-cell chip with a target recovery of 10k cells into the 10x Genomic Chromium machine. After the 10x program finished, 100 µl GEMs per sample were recovered for GEM-RT incubation. GEM-RT cDNA was further cleaned up and amplified with 12 cycles. Samples were determined as passing the QC with fragments ranging from 300 to 9,000bp. 20 µl cDNA per sample was used as input for library generation. After the cDNA fragmentation, end repair, and A-tailing, the adapter was ligated for amplification. Sample index was used for additional 14 PCR cycles. PCR products were cleaned up and size selected, and samples were determined to pass the QC with a size range from 300 to 600bp. Samples with the same mass were multiplexed and sent for sequencing.

value: Cortex

value: Upf2fl/fl Emx1-Cre+


title: EB-hTBLC-D8

value: WT


title: CSKN_NEG_2

value: not edited


title: YY1_Cut&Run_LPKO_Vector_LCL_Rep2


title: CSKN_NEG_18


title: HDF, wound exudate WE224, replicate 1

value: skin

value: wound exudate from diabetic foot ulcer


title: CSP11-Z-2

value: leaves

value: tissue

value: treatment

value: NlCSP11 infiltrated leaves


title: EB-hTBLC-D5

value: hESC


title: YY1_Cut&Run_LPKO_Vector_LCL_Rep1


title: E15.5 Upf2fl/fl Emx1-Cre- mouse cortex

description:
Ctrl
10x Genomics

value: Upf2fl/fl Emx1-Cre-


title: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_4]

description: 10x Genomics

data_processing:
Cell Ranger (version 5.0.1, reference genome: mm10-2020-A<based on Gencode vM23, and filtering out pseudogenes, TEC, miRNA etc. a total of 32285 genes) was used to perform alignment, filtering, barcode counting, and UMI counting for single cell RNA-Seq.
Assembly: mm10

growth_protocol: Mouse NPCs were cultured in DMEM/F12 media with 1x B27 and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
72 hours after the infection, NPCs were dissociated with 1x TrypLE Express and resuspended in 1x PBS with 0.04% BSA.
NPCs were loading the single cell chip with a target recovery of 10k cells into the 10x Genomic Chromium machine, as the GFP group was loaded with 23.6 µl NPCs with 19.6 µl H2O and Cre group had 33 µl NPCs with 10.2 µl H2O. After the 10x program finished, 100 µl GEMs per sample were recovered for GEM-RT incubation. GEM-RT cDNA was further cleaned up and amplified with 12 cycles. Samples were determined as passing the QC with fragments ranging from 300 bp to 9,000 bp, and the concentration for GFP was 15.17 ng/µl while Cre was 14.27 ng/µl. 20 µl cDNA per sample was used as input for library generation. After the cDNA fragmentation and end repair & A-tailing, the adapter was ligated for amplification. Different sample indices (indices from 10x index plate or indices synthesized by IDT)  were used for additional 14 PCR cycles. PCR products were cleaned up and size selected, and samples were determined to pass the QC with a size range from 300 to 600 bp. Samples with the same mass were multiplexed and sent for sequencing.

treatment_protocol: 10 µl GFP or CRE lentivirus were added to 500 µl medium with 4 µg/ml protamine sulfate per well for treatemtn of 400k NPCs per well in a 12-well plate for 24 hours, then 350k NPCs per well were replate to a pre-coated 6 well plate.

value: Neural progenitor cells

value: CRE-LV infection

tag: strain background


title: YY1_Cut&Run_LPKO_LRM_Mutant_LCL_Rep2

value: LCL

value: YY1 (CST, D5D9Z)

value: LRM Mutant


title: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_3]

description: 10x Genomics

value: Cortex


title: EB-hTBLC-D2

value: cultured in E6 medium


title: IgG_Cut&Run_LPKO_EBNALP_LCL_Rep1

value: IgG (Epicypher, 13-0042)

value: LPKO

value: EBNA-LP


title: WIBR3-E8-Rp2

value: WT

value: cultured in E8 medium


title: YY1_Cut&Run_LPKO_LRM_Mutant_LCL_Rep1


title: WIBR3-E8-r108h


title: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_2]

description: 10x Genomics


title: Sample_GLUT3-1_IGO_13922_B_7

city: New York

first: Yuzhe

last: Shi

address: 1250 First Avenue

department: Immunolgy

institute: Memorial Sloan Kettering Cancer Center

data_processing:
DESeq2 was used for normalization and differential analysis of transcriptional data
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: primary T cell

extract_protocol:
RNA was extracted by RNeasy kit and quality control measured by Agilent BioAnalyser
2 ng RNA with integrity numbers ranging from 9.1 to 9.3 underwent amplification using the SMART-seq v4 Ultra Low Input RNA Kit (63488, Clonetech) with 12 cycles of amplification: 95°C for 60 s, 12 times (98°C for 10 s, 65°C for 30 s, 68°C for 180 s) and 72°C for 10 min. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (KK8504, Kapa Biosystems) using 8 cycles of PCR. The final DNA library was double-size purified (0.8-1x) with Ampure XP beads (Beckman coulter)

value: primary T cell

value: CAR T cell


title: Sample_GLUT3-3_IGO_13922_B_9


title: Sample_GLUT3-2_IGO_13922_B_8


title: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_1]

description: 10x Genomics


title: WIBR3-E8-r96h


title: YY1_Cut&Run_LPKO_EBNALP_LCL_Rep3


title: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_10x_2]

description: 10x Genomics


title: Sample_GLUT1-2_IGO_13922_B_5


title: WIBR3-E8-r84h


title: YY1_Cut&Run_LPKO_EBNALP_LCL_Rep2


title: Sample_GLUT1-1_IGO_13922_B_4


title: WIBR3-E8-r72h


title: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_4]

description: 10x Genomics

value: GFP-LV infection


title: YY1_Cut&Run_LPKO_EBNALP_LCL_Rep1


title: Sample_LNGFR-3_IGO_13922_B_3

value: LNGFR


title: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_3]

description: 10x Genomics


title: 889_NoDox_Plastic

city: Nutley

first: Kevin

last: Tong

address: 111 Ideation Way

institute: Hackensack Meridian Health

data_processing:
Files were processed using Kallisto and DESeq2 for differential gene expression analysis. Genes were filtered for significantly regulated genes (Log2FC > 1.0 or < -1.0, adjp-value <0.05)
Assembly: mm9
Supplementary files format and content: TXT files include FPKM and DESeq readouts (Dox vs. NoDox) for samples

source_name: Small intestine

growth_protocol: Organoids were passaged and cultured in 1x CCM for 48 hours prior to collection for RNA-Seq.

extract_protocol:
Organoids were collected and resuspended in Trizol. RNA was extracted using the RNeasy Kit (QIAGEN).
1ug of RNA was submitted to BGI for library construction

treatment_protocol: Vehicle or 4ug/mL doxycycline

value: Small intestine

value: Organoid

value: Untreated


title: WIBR3-E8-r64h

extract_protocol:
RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: hESC


title: Sample_LNGFR-2_IGO_13922_B_2


title: WIBR3-E8-r56h


title: Sample_LNGFR-1_IGO_13922_B_1


title: 700_NoDox_Plastic


title: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_2]

description: 10x Genomics

value: Neural progenitor cells


title: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_1]

description: 10x Genomics


title: WIBR3-E8-r48h


title: WIBR3-E8-r40h


title: 700_Dox_Plastic

value: 4ug/mL Doxycycline


title: 889_Dox_Plastic


title: EB-hTBLC-D15


title: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_10x_1]

description: 10x Genomics

value: Cortex


title: E13.5 Upf2fl/+ Emx1-Cre- mouse cortex [Emxi_9]

data_processing:
The raw data was mapped using STAR.
We calculated the gene-level read counts and identified differentially expressed genes by in-house script.
Assembly: mm10

extract_protocol:
Mouse cortex were dissected out from E13.5 mouse embryos and transfer to 1.5 ml tubes. 1 ml of TRIzol was directly added to the tubes to extract total RNA following the manufacturer protocol. DNase treatment was performed at 37 ºC for 35 min to degrade residue genomic DNA after TRIzol RNA isolation with 1 unit of Turbo DNase per 10 µg total RNA. Following the DNase treatment, RNA was purified again using phenol-chloroform pH 4.5. RNA concentrations were measured using a Nanodrop 2000c. All samples passed the QC test in the bioanalyzer analysis with a RIN of at least 9.0.
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits according to the manufacturer protocol.

tag: developmental stage

value: Upf2fl/+ Emx1-Cre-


title: E13.5 Upf2fl/+ Emx1-Cre- mouse cortex [Emxi_8]


title: MED30&MYCOE_1

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

data_processing:
The sequencing reads were trimed by Trim Galore. The adapter sequence to be trimed was selected as “automatic detection” for the first round and the “Illumina small adapters” for the second round(Galaxy Version 0.6.7+galaxy0). Then the reads were mapped to hg38 Refseq database by using Bowtie2 and counted over the entire gene body (transcript) on the sense strand with respect to the gene orientation by using Featurecounts (Galaxy Version 2.0.3+galaxy1). Deseq2 (Galaxy Version 2.11.40.8+galaxy0) was then used to compute the significance of the differential gene expression.
Assembly: hg38
Supplementary files format and content: reads per gene
Library strategy: PRO-seq

source_name: MIA PaCa-2

extract_protocol:
For nuclei isolation, cells were incubated with swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl2 and 3 mM CaCl2) for 5 min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100 μl of freezing buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA).
For the run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM dithiothreitol, 20 units of SUPERase•In, 1% sarkosyl, and 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30 °C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (10296010, Invitrogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (88816, Thermo Fisher). Purified RNA was treated with PNK before being used for complementary DNA synthesis by using the NEBNext Multiplex Small RNA Library Prep Set for Illumina Kit (E7300S, NEB). Obtained complementary DNA template was amplified by PCR using the Phusion High-Fidelity enzyme (M0530L, NEB) for deep sequencing.

value: MIA PaCa-2

tag: expression


title: Ctl-2_for_MED30&MYCOE


title: MED30&MYCOE_2


title: 560_Dox_Plastic


title: Ctl-1_for_MED30&MYCOE


title: E13.5 Upf2fl/fl Emx1-Cre+ mouse cortex [Emxi_5]

value: Upf2fl/fl Emx1-Cre+


title: CSKN_NEG_12

value: hiPSC derived excitatory neurons

value: not edited


title: WIBR3-E8-r32h

value: WT

value: cultured in E8 medium


title: 889SBTumorNoDox_BME


title: WIBR3-E8-r28h


title: MYCOE_2

value: MYCOE


title: 889SBTumorDox_BME


title: E13.5 Upf2fl/fl Emx1-Cre+ mouse cortex [Emxi_4]


title: 700SBTumorNoDox_BME


title: WIBR3-E8-r24h


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UP_C9]

growth_protocol: For NPCs samples, 200k Upf2fl/fl or Upf2fl/fl Trp53fl/fl NPCs per well were plated in a pre-coated 6 well plate and were cultured in DMEM/F12 media with 1x B27 and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
72 hours after the infection, media was removed from the well and 1 ml TRIzol was added to each well to extract total RNA following the manufacturer protocol. DNase treatment was performed at 37 ºC for 35 min to degrade residue genomic DNA after TRIzol RNA isolation with 1 unit of Turbo DNase per 10 µg total RNA. Following the DNase treatment, RNA was purified again using phenol-chloroform pH 4.5. RNA concentrations were measured using a Nanodrop 2000c. All samples passed the QC test in the bioanalyzer analysis with a RIN of at least 9.0.
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits according to the manufacturer protocol.

treatment_protocol: Mock group was set to add the same volume of NPC media, while Cre group was added with a MOI= 400k in 1 ml NPC media. 14 hours after the plate and infection, AAV contained media was removed and replaced with 2 ml fresh NPC media.

value: Upf2fl/fl Trp53fl/fl

value: AAV9-Cre infection


title: WIBR3-E8-r16h


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UP_C8]


title: 700SBTumorDox_BME

value: Small intestine


title: 560_NoDox_Plastic

value: Organoid


title: Ctl-1_for_MYCOE


title: 682SBTumorNoDox_BME

value: Untreated


title: WIBR3-E8-r12h

value: hESC


title: WIBR3-E8-r36h


title: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UP_C6]

value: Neural progenitor cells


title: WIBR3-E8-r8h


title: 682SBTumorDox_BME

value: 4ug/mL Doxycycline (Mock)


title: WIBR3-E8-r6h


title: MED30OE_2


title: MED30OE_1